Underground structures in liquefiable ground are prone to serious seismic damage in earthquakes. A detailed numerical dynamic analysis is conducted based on a large cross-section underground transportation hub structure in a layered saturated ground with a large distribution of liquefiable soil layers, and another dynamic analysis is conducted in comparison where the soil layers are simulated by a simple linear elastic model with the same modulus distribution as the liquefiable soil layers at peak response. The analysis results show that the seismic deformation and internal force distribution of the underground structure in the two types of ground are distinctly different. In liquefiable ground, the structure’s vertical components located closer to the structure boundaries are subjected to greater responses than those located further away, and the vertical components on the middle floors exhibit relatively large seismic response. Comparison shows that the structure seismic response difference in the two types of soil layers is caused by the different distribution of the dynamic interaction between soil layers and underground structures.